#NEXUS [written Thu Sep 24 17:14:29 JST 2020 by Mesquite version 3.61 (build 927) at tsutsumichie-no-iMac.local/202.220.64.189] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=14; TAXLABELS Osmunda_regalis_R10 Osmunda_japonica_J3J5J6J7J8 Osmunda_japonica_J2J4 Osmunda_japonica_J1 Osmunda_regalis_R15R16R17R18 Osmunda_regalis_R13R14 Osmunda_lancea_L1L3 Osmunda_lancea_L2 Osmunda_regalis_R5R6R7R8R9 Osmunda_regalis_R1R2R3R4 Osmunda_regalis_R11R12 Plenasium_banksiifolium Claytosmunda_claytoniana_CL96 Claytosmunda_claytoniana_CL99 ; END; BEGIN CHARACTERS; TITLE Character_Matrix; DIMENSIONS NCHAR=553; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Osmunda_regalis_R10 AGAGCCAGAGAAGCTGGCTGGTCCACTTCTGGCTGATACATATGTTACTCTGCTGAAGGGAAGGAATGCATGGTATGGCCAGAAGCTTGCGCAAGGGGAGCTTAGACCAGATATGGGAGATAGTATTCAAGGAAAAGGAATGATTCAGGTTGGTACTCAGTGGATTTGGTTTTCTGGAATGTTTAAAGTGTCATTACATGATTCAGTAAAGTGGGTACTTGCCTCCATTCCCTTT--CTGACACAGCAGACCACAACAAGATCGATCATGCATACATGATAAAGAGGAAAAGCAGAATACTACCTTATCATAGAGGGTAAAAATGTGAGACATAGGGACAAGATCACATGTTGCAGTGTATCCCTGAACAGGACTGTAACCAATTTCTTAGCCAAGTTGAAATGCTGCCGTTTGATTAGT-GGACTGGCTGAAGTTTGCAAGGATCATCTGGGTTGCATATTC--TCTGCATTTGAATTTGAATGAGGGTATACGTTAAGGTGTACATTTGTATGTGTGTGTCTCATGCTGTTTTAGTGCTGTATCTAAGAAA Osmunda_japonica_J3J5J6J7J8 AGAGCCAGAGAAGCTGGCTGGTCCACTTCTGGCTGATACATATGTTACTCTGCTGAAGGGAAGGAATGCATGGTATGGCCAGAAGCTTGCGCAAGGGGAGCTTAGACCAGATATGGGAGATAGTATTCAAGGAAAAGGAATGATTCAGGTTGGTACTCATTGGATTTGGTTTTCTGGAATGTTTTAAGTGTCATTACATGATTCAGTAAAGTGGGTACTTGCCTCCATTCCCTTT--CTGACACAGCAGACCACAACAAGATCGATCATGCATACATGATAAAGAGGAAAAGCAGAATACTACCTTATCATAGAGGGTAAAAATATGAGACATAGGGACAAGATCACATGTTGCAGTGTATCCCTGAACGGGACTGTAACCAATTTCTTAGCCAAGTTGAAATGCTGCAGTTTGATTAGT-GGACTGGCTGAAGTTTGCAAGGATCATCTGGGTTGCACATTC--TCTGCATTTGAATTTGAATGAGGGTATACGTTAAGGTGTACATTTGTATGTGTGTGTCTCATGCTGTTTTAGTGCTGTATCTAAGAAA Osmunda_japonica_J2J4 AGAGCCAGAGAAGCTGGCTGGTCCACTTCTGGCTGATACATATGTTACTCTGCTGAAGGGAAGGAATGCATGGTATGGCCAGAAGCTTGCGCAAGGGGAGCTTAGACCAGATATGGGAGATAGTATTCAAGGAAAAGGAATGATTCAGGTTGGTACTCATTGGATTTGGTTTTCTGGAATGTTTTAAGTGTCATTACATGATTCAGTAAAGTGGGTACTTGCCTCCATTCCCTTT--CTGACACAGCAGACCACAACAAGATCGATCATGCATACATGATAAAGAGGAAAAGCAGAATACTACCTTATCATAGAGGGTAAAAATGTGAGACATAGGGACAAGATCACATGTTGCAGTGTATCCCTGAACGGGACTGTAACCAATTTCTTAGCCAAGTTGAAATGCTGCAGTTTGATTAGT-GGACTGGCTGAAGTTTGCAAGGATCATCTGGGTTGCATATTC--TCTGCATTTGAATTTGAATGAGGGTATACATTAAGGTGTACATTTGTATGTGTGTGTCTCATGCTGTTTTAGTGCTGTATCTAAGAAA Osmunda_japonica_J1 AGAGCCAGAGAAGCTGGCTGGTCCACTTCTGGCTGATACATATGTTACTCTGCTGAAGGGAAGGAATGCATGGTATGGCCAGAAGCTTGCGCAAGGGGAGCTTAGACCAGATATGGGAGATAGTATTCAAGGAAAAGGAATGATTCAGGTTGGTACTCATTGGATTTGGTTTTCTGGAATGTTTTAAGTGTCATTACATGATTCAGTAAAGTGGGTACTTGCCTCCATTCCCTTT--CTGACACAGCAGACCACAACAAGATCGATCATGCATACATGATAAAGAGGAAAAGCAGAATACTACCTTATCATAGAGGGTAAAAATGTGAGACATAGGGACAAGATCACATGTTGCAGTGTATCCCTGAACGGGACTGTAACCAATTTCTTAGCCAAGTTGAAATGCTGCAGTTTGATTAGT-GGACTGGCTGAAGTTTGCAAGGATCATCTGGGTTGCATATTC--TCTGCATTTGAATTTGAATGAGGGTATACGTTAAGGTGTAC----------GTGTGTCTCATGCTGTTTTAGTGCTGTATCTAAGAAA Osmunda_regalis_R15R16R17R18 AGAGCCAGAGAAGCTGGCTGGTCCACTTCTGGCTGATACATATGTTACTCTGCTGAAGGGAAGGAATGCATGGTATGGCCAGAAGCTTGCGCAAGGGGAGCTTAGACCAGATATGGGAGATAGTATTCAAGGAAAAGGAATGATTCAGGTTGGTACTCATTGGATTTGGTTTTCTGGAATGTTTTAAGTGTCATTACATGATTCAGTAAAGTGGGTACTTGCCTCCATTCCCTTT--CTGACACAGCAGACCACAACAAGATCGATCATGCATACATGATAAAGAGGAAAAGCAGAATACTACCTTATCATAGAGGGTAAAAATGTGAGACATAGGGACAAGATCACATGTTGCAGTGTATCCCTGAACGGGACTGTAACCAATTTCTTAGCCAAGTTGAAATGCTGCAGTTTGATTAGT-GGACTGGCTGAAGTTTGCAAGGATCATCTGGGTTGCATATTC--TCTGCATTTGAATTTGAATGAGGGTATACGTTAAGGTGTACATTTGTATGTGTGTGTCTCATGCTGTTTTAGTGCTGTATCTAAGAAA Osmunda_regalis_R13R14 AGAGCCAGAGAAGCTGGCTGGTCCACTTCTGGCTGATACATATGTTACTCTGCTGAAGGGAAGGAATGCATGGTATGGCCAGAAGCTTGCGCAAGGGGAGCTTAGACCAGATATGGGAGATAGTATTCAAGGAAAAGGAATGATTCAGGTTGGTACTCAGTGGATTTGGTTTTCTGGATTGTTTTAAGTGTCATTACATGATTCAGTAAAGTGGGTACTTGCCTCCATTCCCTTT--CTGACACAGCAGACCACAACAAGATCGATCATGCATACATGATAAAGAGGAAAAGCAGAATACTACCTTATCATAGAGGGTAAAAATGTGAGACATAGGGACAAGATCACATGTTGCAGTGTATCCCTGAACGGGACTGTAACCAATTTCTTAGCCAAGTTGAAATGCTGCAGTTTGATTAGT-GGACTGGCTGAAGTTTGCAAGGATCATCTGGGTTGCATATTC--TCTGCATTTGAATTTGAATGAGGGTATACGTTAAGGTGTACATTTGTATGTGTGTGTCTCATGCTGTTTTAGTGCTGTATCTAAGAAA Osmunda_lancea_L1L3 AGAGCCAGAGAAGCTGGCTGGTCCACTTCTGGCTGATACATATGTTACTCTGCTGAAGGGAAGGAATGCATGGTATGGCCAGAAGCTTGCGCAAGGGGAGCTTAGACCAGATATGGGAGATAGTATTCAAGGAAAAGGAATGATTCAGGTTGGTACTCATTGGATTTGGTTTTCTGGAATGTTTTAAGTGTCATTACATGATTCAGTAAAGTGGGTACTTGCCTCCATTCCCTTT--CTGACACAGCAGACCACAACAAGATCGATCATGCATACATGATAAAGAGGAAAAGCAGAATACTACCTTATCATAGAGGGTAAAAATATGAGACATAGGGACAAGATCACATGTTGCAGTGTATCCCTGAACGGGACTGTAACCAATTTCTTAGCCAAGTTGAAATGCTGCAGTTTGATTAGT-GGACTGGCTGAAGTTTGCAAGGATCATCTGGGTTGCAAATTC--TCTGCATTTGAATTTGAATGAGAGTATACGTTAAGGTGTACATTTGTATGTGTGTGTCTCATGCTGTTTTAGTGCTGTATCTAAGAAA Osmunda_lancea_L2 AGAGCCAGAGAAGCTGGCTGGTCCACTTCTGGCTGATACATATGTTACTCTGCTGAAGGGAAGGAATGCATGGTATGGCCAGAAGCTTGCGCAAGGGGAGCTTAGACCAGATATGGGAGATAGTATTCAAGGAAAAGGAATGATTCAGGTTGGTACTCATTGGATTTGGTTTTCTGGAATGTTTTAAGTGTCATTACATGATTCAGTAAAGTGGGTACTTGCCTCCATTCCCTTT--CCGACACAGCAGACCACAACAAGATCGATCATGCATACATGATAAAGAGGAAAAGCAGAATACTACCTTATCATAGAGGGTAAAAATATGAGACATAGGGACAAGATCACATGTTGCAGTGTATCCCTGAACGGGACTGTAACCAATTTCTTAGCCAAGTTGAAATGCTGCAGTTTGATTAGT-GGACTGGCTGAAGTTCGCAAGGATCATCTGGGTTGCAAATTC--TCTGCATTTGAATTTGAATGAGAGTATACGTTAAGGTGTACATTTGTATGTGTGTGTCTCATGCTGTTTTAGTGCTGTATCTAAGAAA Osmunda_regalis_R5R6R7R8R9 AGAGCCAGAGAAGCTGGCTGGTCCACTTCTGGCTGATACATATGTTACTCTGCTGAAGGGAAGGAATGCATGGTATGGCCAGAAGCTTGCGCAAGGGGAGCTTAGACCAGATATGGGAGATAGTATTCAAGGAAAAGGAATGATTCAGGTTGGTACTCAGTGGATTTGGTTTTCTGGAATGTTTTAAGTGTCATTACATGATTCAGTAAAGTGGGTACTTGCCTCCATTCCCTTT--CTGACACAGCAGACCACAACAAGATCGATCATGCATACATGATAAAGAGGGAAAGCAGAATACTACCTTATCATAGAGGGTAAAAATGTGAGACATAGGGACAAGATCACATGTTGCAGTGTATCCCTGAACGGGACTGTAACCTATTTCTTAGCCAAGTTGAAATGCTGCAGTTTGATTAGT-GGACTGGCTGAAGTTTGCAAGGATCATCTGGGTTGCATATTC--TCTGCATTTGAATTTGAATGAGGGTATACGTTAAGGTGTACATTTGTATGTGTGTGTCTCATGCTGTTTTAGTGCTGTATCTAAGTAA Osmunda_regalis_R1R2R3R4 AGAGCCAGAGAAGCTGGCTGGTCCACTTCTGGCTGATACATATGTTACTCTGCTGAAGGGAAGGAATGCATGGTATGGCCAAAAGCTTGCGCAAGGGGAGCTTAGACCAGATATGGGAGATAGTATTCAAGGAAAAGGAATGATTCAGGTTGGTACTCAGTGGATTTGGTTTTCTGGAATGTTTTAAGTGTCATTACATGATTCAGTAAAGTGGGTACTTGCCTCCATTCCCTTT--CTGACACAGCAGACCACAACAAGATCGATCATGCATACATGATAAAGAGGAAAAGCAGAATACTACCTTATCATAGAGGGTAAAAATGTGAGACATAGGGACAAGATCACATGTTGCAGTGTATCCCTGAACGGGACTGTAACCAATTTCTTAGCCAAGTTGAAATGCTGCAGTTTGATTAGT-GGACTGGCTGAAGTTTGCAAGGATCATCTGGGTTGCATATTC--TCTGCATTTGAATTTGAATGAGGGTATACGTTAAGGTGTACATTTGTATGTGTGTGTCTCATGCTGTTTTAGTGCTGTATCTAAGAAA Osmunda_regalis_R11R12 AGAGCCAGAGAAGCTGGCTGGTCCACTTCTGGCTGATACATATGTTACTCTGCTGAAGGGAAGGAATGCATGGTATGGCCAGAAGCTTGCGCAAGGGGAGCTTAGACCAGATATGGGAGATAGTATTCAAGGAAAAGGAATGATTCAGGTTGGTACTCAGTGGATTTGGTTTTCTGGAATGTTTAAAGTGTCATTACATGATTCAGTAAAGTGGGTACTTGCCTCCATTCCCTTT--CTGACACAGCAGACCACAACAAGATCGATCATGCATACATGATAAAGAGGAAAAGCAGAATACTACCTTATCATAGAGGGTAAAAGTGTGAGACATAGGGACAAGATCACATGTTGCAGTGTATCCCTGAACCGGACTGTAACCAATTTCTTAGCCAAGTTGAAATGCTGCAGTTTGATTAGT-GGACTGGCTGAAGTTTGCAAGGATCATCTGGGTTGCATATTC--TCTGCATTTGAATTTGAATGAGGGTATATGTTAAGGTGTACATTTGTATGTGTGTGTCTCATGCTGTTTTAGTGCTGTATCTAAGAAA Plenasium_banksiifolium AGAGCCAGAGAAGTTGGCTGGTCCACTTCTGGCTGATACGTATGTTACTCTGCTGAAAGGAAGGAATGCATGGTATGGCCAGAAGCTTGCTCAAGGGGAGCTTAGACCAGATATGGGAGATAGCATTCAAGGAAAAGGAATGATTCAGGTTGGTACTCACTGGATTTGGTTTTCTGGATTGTTTCAAGTGTCATTACATGATTCAGTAAAGTGGGTTCTTGCCTCCATTGCCTTTCTCTGACACATCAGACCACAACAAGATCGATCACGCAT---------AGAGGAAAAGCAGAATACTACCTTATCACAGATGGTAAAAATATGAGACATAGGGACAAGATCACATGTTGCAGTGTATCTGCTAAAGGGACTGTAACCAGTTTCTTAGCCAAGTTGAAATGCTTCAGTTTGATTGGTAGGACTGGCTGAAGTTTGCAAGGATCATCTGGGTTGCATATTCTCTCTGCATTTGAATTTGAATGAGGGTATACGCTAAGGTGTACTACTGTA----TGTGTCTCATGTTGTTTTAGTGTAGTATCTAAGaAA Claytosmunda_claytoniana_CL96 AGAGCCAGAGAAGCTGGCTGGTCCTCTTCTGGCCGATACGTATGTTACTTTGCTGAAGGGAAGGAATGCATGGTATGGCCAGAAGCTTGCACAAGGGGAGCTTAGACCAGATATGGGAGATAGTATTCAAGGAAAAGGAATGATTCAGGTTGGTACTTAGTGGATTTGGTTTTCTGGAATGTTTTAAGTGTCATTGCATGATTCAGTAAAGTGGGTACTTGCCTCCATTCCCTTT--CTGACATAACAGACCACAACAAGATCGATCATGCATACTTGATTAAGAGGAAAAGCAGAATACTATCTTACCATAGAGGGTAAAAATGAGAGACATAGGGACAAGATCACATGTTGCAGTGTATCCCCTAAAGGGACTGTAGCCAATTTCTTAGCCAAGTTG-AATGCTGCAGTTTGATTAGTAGGATTGGCTGAAGTTTGCAAGGATCATCTGGGTTGCATATTC--TCTGCATTTGAATTTGAATGAGGGTATACGTTAAGTTGTACATTTGTATGTGTGTGTCTCATGCTGTTTTAGTGCTGTATCTAAGAAA Claytosmunda_claytoniana_CL99 AGAGCCAGAGAAGCTGGCTGGTCCTCTTCTGGCCGATACGTATGTTACTTTGCTGAAGGGAAGGAATGCATGGTATGGCCAGAAGCTTGCACAAGGGGAGCTTAGACCAGATATGGGAGATAGTATTCAAGGAAAAGGAATGATTCAGGTTGGTACTCAGTGGATTTGGTTTTCTGGAATGTTTTAAGTGTCATTGCATGATTCAGTAAAGTGGGTACTTGCCTCCATTCCCTTT--CTGACATAACAGACCACAACAAGATCGATCATGCATACTTGATTAAGAGGAAAAGCAGAATACTATCTTACCATAGAGGGTAAAAATGAGAGACATAGGGACAAGATCACATGTTGCAGTGTATCCCCTAAAGGGACTGTAGCCAATTTCTTAGCCAAGTTG-AATGCTGCAGTTTGATTAGTAGGATTGGCTGAAGTTTGCAAGGATCATCTGGGTTGCATATTC--TCTGCATTTGAATTTGAATGAGGGTATACGTTAAGTTGTACATTTGTATGTGTGTGTCTCATGCTGTTTTAGTGCTGTATCTAAGAAA ; END; BEGIN MRBAYES; Prset statefreqpr = dirichlet ( 1 , 1 , 1 , 1 ); Lset nst = 2 rates = propinv; log start filename = L110.log replace; mcmcp ngen = 10000000 printfreq = 1000 samplefreq = 100 nchains = 4 savebrlens = yes filename = L110Bayes; mcmc; log stop; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1- 553; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1- 553; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1- 553; END; BEGIN TREES; Title L110tree; ID 0174bf2b39b913; LINK Taxa = Taxa; TRANSLATE [0] 1 Osmunda_regalis_R10, [1] 2 Osmunda_japonica_J3J5J6J7J8, [2] 3 Osmunda_japonica_J2J4, [3] 4 Osmunda_japonica_J1, [4] 5 Osmunda_regalis_R15R16R17R18, [5] 6 Osmunda_regalis_R13R14, [6] 7 Osmunda_lancea_L1L3, [7] 8 Osmunda_lancea_L2, [8] 9 Osmunda_regalis_R5R6R7R8R9, [9] 10 Osmunda_regalis_R1R2R3R4, [10] 11 Osmunda_regalis_R11R12, [11] 12 Plenasium_banksiifolium, [12] 13 Claytosmunda_claytoniana_CL96, [13] 14 Claytosmunda_claytoniana_CL99; TREE con_50_majrule = ((13:0.004001,14:0.0022)1.00:0.0204355,(12:0.075165,(6:0.003852,9:0.008235,10:0.004036,(1:0.005482,11:0.008209):0.005225,(3:0.004038,4:0.002087,5:0.00205,(2:0.003134,(7:0.002096,8:0.006109)0.99:0.006085)0.84:0.005279)0.62:0.003975)0.92:0.012282)0.50:0.0204355)[% ] [% ] [% setBetweenBits = selected ]; TREE con_50_majrule = (1:0.005482,11:0.008209,(((2:0.003134,(7:0.002096,8:0.006109):0.006085):0.005279,3:0.004038,4:0.002087,5:0.00205):0.003975,6:0.003852,9:0.008235,10:0.004036,(12:0.075165,(13:0.004001,14:0.0022):0.040871):0.012282):0.005225); END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1600935269806; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 9137453144281948071; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 3930282149288790202; mqVersion 361; checksumv 0 3 1423066533 null getNumChars 553 numChars 553 getNumTaxa 14 numTaxa 14 short true bits 1152921504606846991 states 15 sumSquaresStatesOnly 181633.0 sumSquares 2.3058430092138757E18 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState true false 296; setPopoutState 300; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1959 1120; setLocation 870 211; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; desuppress; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #3930282149288790202 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 0 -72; setLocation 870 211; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; colorCells #mesquite.charMatrices.ColorByState.ColorByState; tell It; setStateLimit 9; toggleUniformMaximum on; endTell; colorRowNames #mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor; colorColumnNames #mesquite.charMatrices.CharGroupColor.CharGroupColor; colorText #mesquite.charMatrices.NoColor.NoColor; setBackground White; toggleShowNames on; toggleShowTaxonNames on; toggleTight off; toggleThinRows off; toggleShowChanges off; toggleSeparateLines off; toggleShowStates on; toggleReduceCellBorders off; toggleAutoWCharNames off; toggleAutoTaxonNames off; toggleShowDefaultCharNames off; toggleConstrainCW on; toggleBirdsEye off; toggleShowPaleGrid off; toggleShowPaleCellColors off; toggleShowPaleExcluded off; togglePaleInapplicable on; togglePaleMissing off; toggleShowBoldCellText off; toggleAllowAutosize off; toggleColorsPanel off; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; getWindow; tell It; forceAutosize; endTell; hideWindow; getEmployee #mesquite.charMatrices.AlterData.AlterData; tell It; toggleBySubmenus off; endTell; getEmployee #mesquite.charMatrices.ColorCells.ColorCells; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel; tell It; togglePanel off; endTell; getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector; tell It; autotabOff; endTell; getEmployee #mesquite.charMatrices.SelSummaryStrip.SelSummaryStrip; tell It; showStrip off; endTell; getEmployee #mesquite.align.AlignToDropped.AlignToDropped; tell It; gapCosts 16 6 1 1; subCosts 10 5 10 10 10 5 5 10 10 10 5 10; endTell; getEmployee #mesquite.molec.ColorByAA.ColorByAA; tell It; emphasizeDegeneracy off; endTell; getEmployee #mesquite.molec.SequenceInfoEditor.SequenceInfoEditor; tell It; panelOpen false; endTell; endTell; endTell; endTell; end;